From patchwork Thu Apr 29 12:22:43 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Roel Janssen X-Patchwork-Id: 28979 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 0734227BC7C; Thu, 29 Apr 2021 13:34:02 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.9 required=5.0 tests=BAYES_00,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 65AD027BC7D for ; Thu, 29 Apr 2021 13:33:58 +0100 (BST) Received: from localhost ([::1]:53510 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lc5rh-0003tf-Jl for patchwork@mira.cbaines.net; Thu, 29 Apr 2021 08:33:57 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:44312) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lc5i6-0004HZ-Ge for guix-patches@gnu.org; Thu, 29 Apr 2021 08:24:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43479) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lc5i6-0000yq-6v for guix-patches@gnu.org; Thu, 29 Apr 2021 08:24:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lc5i6-00056u-2Y for guix-patches@gnu.org; Thu, 29 Apr 2021 08:24:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47930] [PATCH] gnu: Add pbgzip. Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 29 Apr 2021 12:24:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47930 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Efraim Flashner , Maxime Devos , Xinglu Chen Cc: 47930@debbugs.gnu.org Received: via spool by 47930-submit@debbugs.gnu.org id=B47930.161969898519581 (code B ref 47930); Thu, 29 Apr 2021 12:24:02 +0000 Received: (at 47930) by debbugs.gnu.org; 29 Apr 2021 12:23:05 +0000 Received: from localhost ([127.0.0.1]:55025 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lc5h6-00055E-Ag for submit@debbugs.gnu.org; Thu, 29 Apr 2021 08:23:05 -0400 Received: from eggs.gnu.org ([209.51.188.92]:35872) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lc5h3-000551-O0 for 47930@debbugs.gnu.org; Thu, 29 Apr 2021 08:22:59 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:41206) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lc5gw-0000VY-K5; Thu, 29 Apr 2021 08:22:50 -0400 Received: from [143.121.198.253] (port=58448) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_128_CBC_SHA1:128) (Exim 4.82) (envelope-from ) id 1lc5gv-0001QS-EF; Thu, 29 Apr 2021 08:22:49 -0400 References: <874kfz71ni.fsf@yoctocell.xyz> From: Roel Janssen Message-ID: Date: Thu, 29 Apr 2021 14:22:43 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.7.1 MIME-Version: 1.0 In-Reply-To: Content-Language: en-US X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches On 4/29/21 9:29 AM, Efraim Flashner wrote: > On Thu, Apr 22, 2021 at 06:40:46PM +0200, Maxime Devos wrote: >> Xinglu Chen schreef op wo 21-04-2021 om 23:45 [+0200]: >>> On Wed, Apr 21 2021, Roel Janssen wrote: >>> >>>> [...] >>>> + (arguments >>>> + `(#:phases >>>> + (modify-phases %standard-phases >>>> + (add-after 'unpack 'autogen >>>> + (lambda _ >>>> + (zero? (system* "sh" "autogen.sh"))))))) >>> IIRC, phases don’t have to return #t, so you could remove ‘zero?’. >> Try running (system* "does-not-exist"). It will fail by returning >> something non-zero. If I recall how to call "invoke" correctly, >> I would recommend (invoke "sh" "autogen.sh") here. "invoke" raises >> an exception when the command fails, instead of returning something. > While we're at it, can this phase replace 'bootstrap? It seems to me we > shouldn't need both phases. This indeed seems to be the best thing to do.  I attached a new patch. I had to leave autoconf and automake in the native-inputs because otherwise the command "aclocal" and "autom4te" couldn't be found. Thanks all for the feedback!  I hope this new patch is fine. Kind regards, Roel Janssen From b03f8d8926cdd6a28502f2bdc6db74854144f050 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 29 Apr 2021 14:18:30 +0200 Subject: [PATCH] gnu: Add pbgzip. * gnu/packages/bioinformatics.scm (pbgzip): New variable. --- gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++- 1 file changed, 35 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 83ebfc2d8f..8c4d0fc649 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins ;;; Copyright © 2015 Andreas Enge -;;; Copyright © 2016, 2020 Roel Janssen +;;; Copyright © 2016, 2020, 2021 Roel Janssen ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner ;;; Copyright © 2016, 2020 Marius Bakke ;;; Copyright © 2016, 2018 Raoul Bonnal @@ -571,6 +571,40 @@ input and output BAMs must adhere to the PacBio BAM format specification. Non-PacBio BAMs will cause exceptions to be thrown.") (license license:bsd-3))) +(define-public pbgzip + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) + (package + (name "pbgzip") + (version (string-take commit 7)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nh13/pbgzip") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/nh13/pbgzip") + (synopsis "Parallel Block GZIP") + (description "This package implements parallel block gzip. For many +formats, in particular genomics data formats, data are compressed in +fixed-length blocks such that they can be easily indexed based on a (genomic) +coordinate order, since typically each block is sorted according to this order. +This allows for each block to be individually compressed (deflated), or more +importantly, decompressed (inflated), with the latter enabling random retrieval +of data in large files (gigabytes to terabytes). @code{pbgzip} is not limited +to any particular format, but certain features are tailored to genomics data +formats when enabled. Parallel decompression is somewhat faster, but truly the +speedup comes during compression.") + (license license:expat)))) + (define-public blasr-libcpp (package (name "blasr-libcpp") -- 2.31.1